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- PDB-6af7: DJ-1 C106S unbound -

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Basic information

Entry
Database: PDB / ID: 6af7
TitleDJ-1 C106S unbound
ComponentsProtein/nucleic acid deglycase DJ-1
KeywordsHYDROLASE / DJ-1 / Parkinson's disease / Drug discovery / Fragment-based drug discovery
Function / homology
Function and homology information


positive regulation of acute inflammatory response to antigenic stimulus / tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / guanine deglycation, glyoxal removal / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization ...positive regulation of acute inflammatory response to antigenic stimulus / tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / guanine deglycation, glyoxal removal / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization / negative regulation of death-inducing signaling complex assembly / negative regulation of TRAIL-activated apoptotic signaling pathway / positive regulation of L-dopa biosynthetic process / glyoxalase (glycolic acid-forming) activity / negative regulation of protein K48-linked deubiquitination / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / glycolate biosynthetic process / detection of oxidative stress / glyoxal metabolic process / guanine deglycation / methylglyoxal metabolic process / detoxification of mercury ion / ubiquitin-protein transferase inhibitor activity / protein deglycase / mercury ion binding / hydrogen peroxide metabolic process / positive regulation of dopamine biosynthetic process / protein deglycase activity / positive regulation of autophagy of mitochondrion / superoxide dismutase copper chaperone activity / oxidoreductase activity, acting on peroxide as acceptor / positive regulation of mitochondrial electron transport, NADH to ubiquinone / lactate biosynthetic process / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / protein repair / peptidase inhibitor activity / cellular detoxification of aldehyde / peroxiredoxin activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / small protein activating enzyme binding / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / detoxification of copper ion / negative regulation of protein sumoylation / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein export from nucleus / cupric ion binding / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of androgen receptor signaling pathway / membrane hyperpolarization / oxygen sensor activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / insulin secretion / ubiquitin-like protein conjugating enzyme binding / nuclear androgen receptor binding / androgen receptor signaling pathway / ubiquitin-specific protease binding / cytokine binding / dopamine uptake involved in synaptic transmission / positive regulation of reactive oxygen species biosynthetic process / cuprous ion binding / signaling receptor activator activity / membrane depolarization / regulation of synaptic vesicle endocytosis / single fertilization / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of neuron apoptotic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / removal of superoxide radicals / SUMOylation of transcription cofactors / adult locomotory behavior / regulation of mitochondrial membrane potential / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / mitochondrion organization / adherens junction / enzyme activator activity / positive regulation of protein-containing complex assembly / Late endosomal microautophagy / PML body / mitochondrial intermembrane space / autophagy / positive regulation of protein localization to nucleus / kinase binding / cellular response to hydrogen peroxide / Chaperone Mediated Autophagy / positive regulation of reactive oxygen species metabolic process / Aggrephagy / synaptic vesicle / glucose homeostasis / peptidase activity / cell body / cellular response to oxidative stress / regulation of inflammatory response / response to oxidative stress / scaffold protein binding / DNA-binding transcription factor binding
Similarity search - Function
Protein/nucleic acid deglycase DJ-1 / : / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsCaaveiro, J.M.M. / Tashiro, S. / Tsumoto, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)Platform for Drug Discovery, Informatics and Structural Life Science Japan
Japan Society for the Promotion of Science25249115 Japan
Japan Society for the Promotion of Science16H02420 Japan
Japan Society for the Promotion of Science15K06962 Japan
Citation
Journal: ACS Chem. Biol. / Year: 2018
Title: Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
Authors: Tashiro, S. / Caaveiro, J.M.M. / Nakakido, M. / Tanabe, A. / Nagatoishi, S. / Tamura, Y. / Matsuda, N. / Liu, D. / Hoang, Q.Q. / Tsumoto, K.
#1: Journal: Biochemistry / Year: 2014
Title: Thermodynamic and structural characterization of the specific binding of Zn(II) to human protein DJ-1.
Authors: Tashiro, S. / Caaveiro, J.M.M. / Wu, C.X. / Hoang, Q.Q. / Tsumoto, K.
History
DepositionAug 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein/nucleic acid deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1753
Polymers19,9011
Non-polymers2742
Water5,008278
1
A: Protein/nucleic acid deglycase DJ-1
hetero molecules

A: Protein/nucleic acid deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3496
Polymers39,8022
Non-polymers5474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area3450 Å2
ΔGint-35 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.750, 74.750, 75.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-555-

HOH

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Components

#1: Protein Protein/nucleic acid deglycase DJ-1 / Maillard deglycase / Oncogene DJ1 / Parkinson disease protein 7 / Parkinsonism-associated deglycase ...Maillard deglycase / Oncogene DJ1 / Parkinson disease protein 7 / Parkinsonism-associated deglycase / Protein DJ-1 / DJ-1


Mass: 19900.986 Da / Num. of mol.: 1 / Mutation: C106S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Plasmid: pET28B / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q99497, Hydrolases; Acting on ester bonds; Thioester hydrolases, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, protein deglycase
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: pH 8.5, 100mM TRIS-HCl, 200mM sodium citrate, 30% PEG 400, 5mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→26.6 Å / Num. obs: 60285 / % possible obs: 100 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.1
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLM7.0.9data reduction
SCALA3.3.20data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SOA

1soa


Resolution: 1.3→26.6 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.858 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.028 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12038 1836 3 %RANDOM
Rwork0.10016 ---
obs0.10078 58414 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.515 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å20 Å2
3----0.36 Å2
Refinement stepCycle: 1 / Resolution: 1.3→26.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 17 278 1671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191516
X-RAY DIFFRACTIONr_bond_other_d0.0010.021564
X-RAY DIFFRACTIONr_angle_refined_deg1.9842.0032060
X-RAY DIFFRACTIONr_angle_other_deg0.93833643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9515216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50725.6958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44215294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.429158
X-RAY DIFFRACTIONr_chiral_restr0.1340.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211718
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02292
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5261.164779
X-RAY DIFFRACTIONr_mcbond_other1.4571.158778
X-RAY DIFFRACTIONr_mcangle_it1.6421.748980
X-RAY DIFFRACTIONr_mcangle_other1.6411.752981
X-RAY DIFFRACTIONr_scbond_it3.0371.559737
X-RAY DIFFRACTIONr_scbond_other3.0341.559737
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2322.1721065
X-RAY DIFFRACTIONr_long_range_B_refined3.46311.9751949
X-RAY DIFFRACTIONr_long_range_B_other2.98210.3541755
X-RAY DIFFRACTIONr_rigid_bond_restr5.2433080
X-RAY DIFFRACTIONr_sphericity_free34.749567
X-RAY DIFFRACTIONr_sphericity_bonded8.56553267
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.148 152 -
Rwork0.134 4287 -
obs--100 %

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